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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Conservation of Protein Domains02:26

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding01:22

Protein Folding

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Related Experiment Video

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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CPred: a web server for predicting viable circular permutations in proteins.

Wei-Cheng Lo1, Li-Fen Wang, Yen-Yi Liu

  • 1Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan.

Nucleic Acids Research
|June 14, 2012
PubMed
Summary
This summary is machine-generated.

Circular permutation (CP) enables protein engineering by altering termini, but experimental viability is uncertain. This study introduces CPred, a web server predicting viable CP sites to aid research and bioengineering.

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Area of Science:

  • Protein engineering
  • Structural biology
  • Bioinformatics

Background:

  • Circular permutation (CP) rearranges protein structures, altering termini and influencing activity, stability, and function.
  • CP has broad applications in protein research and bioengineering, but its experimental implementation is complex and costly.
  • Predicting viable circular permutation sites is challenging due to the lack of practical computational tools.

Purpose of the Study:

  • To develop an efficient and user-friendly web server for predicting viable circular permutation cleavage sites.
  • To provide a practical computational tool to guide experimental design in protein engineering.

Main Methods:

  • Implementation of a previously designed comprehensive method for predicting viable CP cleavage sites.
  • Development of a web server named CPred (CP site predictor).

Main Results:

  • CPred offers an efficient and user-friendly platform for predicting circular permutation sites.
  • The web server facilitates the identification of feasible positions for creating viable circular permutants.

Conclusions:

  • CPred is expected to promote fundamental research and biotechnological applications of circular permutation.
  • The tool addresses the need for practical computational methods in protein engineering and bioengineering.